| name | ancombc |
| description | ANCOM-BC / ANCOM-BC2 — compositionally aware differential abundance with sampling-fraction bias correction (Bioconductor ANCOMBC). Use when DA must account for compositionality and unequal sampling fractions; complements MaAsLin2/LEfSe. Upstream: https://github.com/FrederickHuangLin/ANCOMBC (Bioconductor ANCOMBC). Route via research-analysis.
|
| license | MIT |
| category | evaluation |
| tags | ["ANCOM-BC","ANCOM-BC2","differential-abundance","compositionality","Bioconductor"] |
| upstream | https://github.com/FrederickHuangLin/ANCOMBC |
| stage | report |
ANCOM-BC / ANCOM-BC2
Upstream: FrederickHuangLin/ANCOMBC ·
Bioconductor: https://bioconductor.org/packages/ANCOMBC/
Citation
Lin, H. & Peddada, S. D. Analysis of compositions of microbiomes with bias
correction. Nat. Commun. 11, 3514 (2020).
https://doi.org/10.1038/s41467-020-17041-7
ANCOM-BC2: Lin, H. & Peddada, S. D. Multigroup analysis of compositions of
microbiomes with covariate adjustments and repeated measures. Nat. Methods
21, 83–89 (2024). https://doi.org/10.1038/s41592-023-02092-7
See also docs/references.md.
Analytical thinking
ANCOM-BC estimates sampling fractions, corrects compositional bias, and
reports taxon-wise effects with CIs and FDR. Prefer when compositionality is a
primary concern. Pin ancombc vs ancombc2, formula, and prevalence filters.
Often takes phyloseq / TreeSummarizedExperiment-style inputs.
| vs | Prefer ANCOM-BC when |
|---|
maaslin2 | Explicit sampling-fraction bias correction focus |
lefse | Modern FDR + CI vs classic LDA |
stamp | R/Bioconductor pipeline vs GUI exploratory tests |
How to run
BiocManager::install("ANCOMBC")
library(ANCOMBC)
Decision tree
Differential abundance?
├─ Bias-corrected compositional DA → ancombc
├─ Multivariable / longitudinal meta-omics → maaslin2
├─ Classic LDA → lefse
└─ GUI exploratory → stamp
Related skills
research-analysis · maaslin2 · lefse · phyloseq · microeco ·
stamp · tool-selection
